search

CAMI-challenge / CAMISIM

CAMISIM: Simulating metagenomes and microbial communities
https://data.cami-challenge.org/participate
Apache License 2.0
166 stars 36 forks source link

[documentation] Give correct arguments to read simulators #53

Open yoann-dufresne opened 5 years ago

yoann-dufresne commented 5 years ago

I'm trying to use CAMISIM to generate a big fastq file containing community reads with no error.

If I understand well, this is possible using wgsim read simulator with the option "errorfree" (I saw that in the code). So, I changed the config file with theses values : readsim=tools/wgsim/wgsim error_profiles=errorfree

But this is not that simple. CAMISIM wants a file as input for the error_profiles value. How can I change the values for a working pipeline ?

I think that it should be nice to have one or more wiki pages to explain the possible values in the config file.

AlphaSquad commented 5 years ago

You are right, there should be a description for every read simulator how to modify the config accordingly, and the way to do this for the wgsim simulator is particularly ugly. I will need to have a look at that.

Having said that, the way it should work right now (changing the following 4 options): readsim=tools/wgsim/wgsim error_profiles=. # CAMISIM expects a directory, but the option is not really required profile=0.0 # error-rate type=wgsim

yazhinia commented 2 years ago

How can we do the error-free or customized error rate with the art_illumina-2.3.6/art_illumina read simulator?

AlphaSquad commented 2 years ago

Error-free can only be done with wgsim (see my comment above for this). It should not make a difference whether you use ART or wgsim here. For using the custom error profiles of ART please have a look at this pull request which describes how to add and use you own trained error profile: https://github.com/CAMI-challenge/CAMISIM/pull/88